Strained germanium-on-silicon (Ge—Si) photodiodes have been favored for their advantages of easy integration, high speed, high absorption coefficient to communication wavelength and CMOS compatibility with silicon waveguides. Conventional Ge—Si photodiodes suffer from large dark current induced by the large lattice mismatch between germanium (Ge) and silicon (Si) materials. The 4.2% lattice mismatch induces a large amount of dislocations and defects along the Ge—Si interface and threading dislocations at the Ge mesa sidewall. As a proper bias is applied through the junction, the intrinsic germanium layer is easily depleted, thus the dislocations and defects are exposed in a strong electric field. Undesirably, this results in a large dark current. Besides, the dark current increases by 40˜60% as temperature increase every 10° C., which will induce significantly performance degradation at high-temperature environment.